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- PDB-2y7p: DntR Inducer Binding Domain in Complex with Salicylate. Trigonal ... -

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Basic information

Entry
Database: PDB / ID: 2y7p
TitleDntR Inducer Binding Domain in Complex with Salicylate. Trigonal crystal form
ComponentsLYSR-TYPE REGULATORY PROTEIN
KeywordsTRANSCRIPTION REGULATOR / DNA-BINDING / TRANSCRIPTION / TRANSCRIPTION FACTOR / TRANSCRIPTION REGULATION
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...: / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-HYDROXYBENZOIC ACID / LysR-type regulatory protein
Similarity search - Component
Biological speciesBURKHOLDERIA SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / S-SAD/MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDevesse, L. / Smirnova, I. / Lonneborg, R. / Kapp, U. / Brzezinski, P. / Leonard, G.A. / Dian, C.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: Crystal Structures of Dntr Inducer Binding Domains in Complex with Salicylate Offer Insights Into the Activation of Lysr-Type Transcriptional Regulators.
Authors: Devesse, L. / Smirnova, I. / Lonneborg, R. / Kapp, U. / Brzezinski, P. / Leonard, G.A. / Dian, C.
History
DepositionFeb 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3504
Polymers24,8521
Non-polymers1,4983
Water3,261181
1
A: LYSR-TYPE REGULATORY PROTEIN
hetero molecules

A: LYSR-TYPE REGULATORY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6998
Polymers49,7042
Non-polymers2,9956
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6130 Å2
ΔGint-23.8 kcal/mol
Surface area18270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.698, 95.698, 67.404
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein LYSR-TYPE REGULATORY PROTEIN


Mass: 24851.852 Da / Num. of mol.: 1 / Fragment: INDUCER BINDING DOMAIN, RESIDUES 90-301 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BURKHOLDERIA SP. (bacteria) / Strain: DNT / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q7WT50
#2: Chemical ChemComp-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O3
#3: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, PHE 90 TO MET
Nonpolymer detailsPEG 8000 (PEU): PEG 8000 USED IN CRYOCOOLING CONDITION. FRAGMENT OF THIS MODELLED IN ELECTRON DENSITY
Sequence detailsSEQUENCE CRYSTALLISED CONTAINS RESIDUES 90 - 301 OF Q7WT50 WITH F90M POINT MUTATION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.2 % / Description: NONE
Crystal growDetails: 0.2 M NA/K TARTRATE, 0.1 M TRIS PH 8.0-8.5; PEG 8000 28-30%

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.82, 0.976
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.821
20.9761
ReflectionResolution: 1.85→52.3 Å / Num. obs: 29716 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 22.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.2
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHELXEphasing
PHASERphasing
RefinementMethod to determine structure: S-SAD/MOLECULAR REPLACEMENT
Starting model: INITIAL S-SAD MODEL

Resolution: 1.85→82.76 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.42 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21599 1526 5 %RANDOM
Rwork0.18001 ---
obs0.18182 28765 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å20 Å2
2---0.72 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.85→82.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 43 181 1928
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221822
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9882471
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04222.5383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33715294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1371516
X-RAY DIFFRACTIONr_chiral_restr0.140.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211400
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1871.51092
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.02321770
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8993730
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.5814.5696
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 118 -
Rwork0.258 2091 -
obs--98.93 %

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